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Workflow and Tool Execution

The execute command provides tools to execute CWL documents locally or on a remote server (soonish™).

Usage

Execution of CWL Files locally or on remote servers

Usage: s4n execute <COMMAND>

Commands:
  local  Runs CWL files locally [aliases: l]      
  make-template  Creates job file template for execution (e.g. inputs.yaml)
  help   Print this message or the help of the given subcommand(s)

Options:
  -h, --help  Print help

execute local

Usage

Runs CWL files locally

Usage: s4n execute local [OPTIONS] <FILE> [ARGS]...

Arguments:
  <FILE>     CWL File to execute
  [ARGS]...  Other arguments provided to cwl file

Options:
      --outdir <OUT_DIR>  A path to output resulting files to
      --quiet             Runner does not print to stdout
      --podman            Use podman instead of docker
  -h, --help              Print help

execute remote

Not yet implemented

execute make-template

s4n execute make-template is able to create a dummy CWL job file (e.g. inputs.yaml) that can be used as a template for an upoming execution of CWL.

Usage

Creates job file template for execution (e.g. inputs.yaml)

Usage: s4n execute make-template <CWL>

Arguments:
  <CWL>  CWL File to create input template for

Options:
  -h, --help  Print help